During the introduction of the game, Cryptosporidium 138 is shown partying at a hippie convention in Golden Gate Park, dancing with young women around him, moments before the destruction of the Mothership and death of Orthopox-13. Seconds afterwards, KGB Agents ambush the party to assassinate Crypto, leading to Crypto having to locate Pox's Holopox Unit in eastern Hashbury, avoiding swarming KGB agents and burning debris from the Mothership. Soon after, Crypto meets up with a stoned hippie called The Freak, who knows events going on in Bay City. Through their discussion, Crypto discovers that hippie guru Coyote Bongwater is teaming up with the KGB to release a new drink named Revelade, which rots out the brainstem to remove traces of Furon DNA. After defeating the KGB protecting Bongwater, he then learns from The Freak that Bongwater is planning to fumigate the city with Revelade-filled gas, leading to Crypto recovering the Datacores needed to repair the Saucer. Once this is done, he uses the Saucer to destroy the blimps before they can pollute the city.
Crypto, after destroying the blimps, learns from Prudence Kane that Bongwater iss going to dump Revelade into the bay via trucks, revealing the location of Coyote Bongwater. After destroying the trucks, he launches an assault on the Old Fort, where he discovers Bongwter, leading to a long battle. Once Bongwater is defeated, he makes a call to KGB agent Agent Oranchov, who reveals that Bay City, now being useless to them, must be destroyed using nukes. After Bongwater is killed by Crypto, he travels to the rock, confronting Oranchov. The KGB agents attempt to assassinate Crypto, only for them to be killed by an undercover spy, who makes their escape. Crypto manages to kill a KGB agent carrying confidential files, which reveals that the KGB are planning to use the nukes, carried in vans, to destroy Bay City. Afterwards, Crypto enters his saucer, where he then drops the vans in the water. Once the nuclear threat was neutralized, he destroys The Rock and departs for Albion to stop Oranchov.
Old Fort: An old fortress located north of the Golden Gate Park, sitting atop a hillside. The fort is impervious to Crypto's weapons and therefore cannot be destroyed. The base is used as Coyote Bongwater's underground lair in "The Alien Who Probed Me", protected by KGB agents from the outside and inside. The base can be accessed from the Old Fort during the mission. After killing Bongwater, Crypto destroys the inner door of the cave to escape. The small area located near it contains several hippie tents (used by The Yappies) and a Landing Zone.
Old Fort Tunnel: A tunnel cutting through a slope, located below the Old Fort. The fort contains a large door that gains access to the base, which is destroyed after defeating Bongwater.
Golden Gate Park: A park north of Hashbury and south of the Old Fort, loosely based on the identically-named park in San Francisco. Golden Gate Park features a prominent number of hippies gathering in communes, tents, protest signs, a wooden concert stage to the northwest decorated with Revelade posters, The Flyppies' territory, a Landing Zone next to a hippie minibus, and an Arkvoodle Cult camp (which appears after "Shama Llama Slips Up" and despawns after "Shearing The Llama"). Golden Gate Park is the first location visited in-game.
Hashbury: A neighborhood south of Golden Gate Park, based on the district Haight-Ashbury in San Francisco, famous for being the birthplace of the hippie subculture The district features several apartment buildings painted with hippie murals, and is heavily populated by hippies. Hashbury is the location of Crypto's first unlocked Landing Zone, and is the location of Bongwater's apartment building. Near the borders of the district and Ginsberg Heights is a small park that sits the first Arkvoodle worship area.
Ginsberg Heights: A residential area located west of Hashbury, home to the upper-class citizens of Bay City. The area features several colourful apartment buildings, commercial buildings and Victorian houses (based on the famous Painted ladies of San Francisco), and one Landing Zone unlocked after completing "Who Is Arkvoodle?". Verity lives southeast of the district.
Coit Tower: A monumental tower based on the identical monument in San Francisco. The tower is located upon a high mountain slope, where the road snakes around. Coit Tower is featured during the odd-job mission "I Left My Parts in San Fran... err... Bay City", where the radio transmitter is placed on top, leading the player to having to hold off attacking military.
Coit Mountain: A high mountain that Coit Tower sits on. The road snakes around the mountain slopes, and is a high-traffic area for Urbans and Policemen.
Coit Tower Tunnel: A tunnel going through a slope near Coit Mountain.
The Wharf: A port north of the Eastern Lowlands. In the south there are several commercial buildings, two Landing Zones (one situated on the nothern mountain, and one near several billboards), Fisherman's Grotto, two piers (one on the western side, one on the eastern), and to the north a mountain. The western pier has soldiers stationed there.
The Rock: The Rock (based upon Alcatraz Island situates an abandoned prison that the KGB use as a base. It is accessed and destroyed during "The Guns of Alcatraz" to weaken the KGB presence in Bay City, although it is rebuilt soon after.
Michael Bay: A bay in Bay City that creates a donut shape, except without a coast to the north. The Rock is in the middle of the bay. The only way, other than travelling via Saucer, to cross the bay is by going to the military pier in The Wharf and flying by Jetpack.